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| PhoneHome : --noPhoneHome, --phoneHomeThinning [100] | | PhoneHome : --noPhoneHome, --phoneHomeThinning [100] |
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− | === Kinship Options === | + | ===Kinship Options === |
| --kinGeno: kinship matrix is estimated from genotype | | --kinGeno: kinship matrix is estimated from genotype |
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| --kinPedigree: kinship matrix is estimated from pedigree structure | | --kinPedigree: kinship matrix is estimated from pedigree structure |
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| --kinFile: kinship matrix is read from a file | | --kinFile: kinship matrix is read from a file |
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| --kinMaf: the maf cutoff for markers used to estimate kinship | | --kinMaf: the maf cutoff for markers used to estimate kinship |
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| --kinMiss: the genotype call rate cutoff for markers included to estimate kinship | | --kinMiss: the genotype call rate cutoff for markers included to estimate kinship |
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| ===Input/Output Options=== | | ===Input/Output Options=== |
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| --ped: merlin format ped file. | | --ped: merlin format ped file. |
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| --dat: merlin format dat file. | | --dat: merlin format dat file. |
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| --vcf: vcf file | | --vcf: vcf file |
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| --groupFile: gene group file for gene level tests | | --groupFile: gene group file for gene level tests |
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| --longOutput: [ON/OFF] turning this option on will include single variants results in gene-level results report also. | | --longOutput: [ON/OFF] turning this option on will include single variants results in gene-level results report also. |
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| --prefix: output file prefix | | --prefix: output file prefix |
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| ===VC options=== | | ===VC options=== |
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| --inverseNormal: trait will be inverse normalized before analysis | | --inverseNormal: trait will be inverse normalized before analysis |
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| --useCovariates: covariates saved in ped file will be adjusted | | --useCovariates: covariates saved in ped file will be adjusted |
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| --traitName: a specified trait that needs to be analyzed. If not specified, then all traits will be analyzed. | | --traitName: a specified trait that needs to be analyzed. If not specified, then all traits will be analyzed. |
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| === Single Variant Tests=== | | === Single Variant Tests=== |
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| --SingleVarScore: the score test | | --SingleVarScore: the score test |
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| ===Burden Tests=== | | ===Burden Tests=== |
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| --burden: the unweighted burden test | | --burden: the unweighted burden test |
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| --MB: the Madsen-Browning weighted burden test | | --MB: the Madsen-Browning weighted burden test |
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| --VT: the variable threshold test | | --VT: the variable threshold test |
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| --SKAT_BETA: the beta density weighted SKAT test (the original test) | | --SKAT_BETA: the beta density weighted SKAT test (the original test) |
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| --SKAT_UW: the unweighted SKAT test | | --SKAT_UW: the unweighted SKAT test |
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| --SKAT_MB: the Madsen-Browning weighted SKAT test | | --SKAT_MB: the Madsen-Browning weighted SKAT test |
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| ===Other Options=== | | ===Other Options=== |
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| --freqFile []: allow users to enter frequency of markers from a file | | --freqFile []: allow users to enter frequency of markers from a file |
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| --annotation: allow users to group variants based on annotation | | --annotation: allow users to group variants based on annotation |
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| --maf: maf cutoff for markers to be grouped for gene-level tests | | --maf: maf cutoff for markers to be grouped for gene-level tests |
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| --miss: the genotype calling missing rate filter before grouping variants for gene-level tests | | --miss: the genotype calling missing rate filter before grouping variants for gene-level tests |
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| --simulate: allows an integer for number of permutations requested in single variant score test | | --simulate: allows an integer for number of permutations requested in single variant score test |
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| --dosage: the flag to tell use dosage saved in VCF file, instead of genotype | | --dosage: the flag to tell use dosage saved in VCF file, instead of genotype |
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| --founderFreq: use founder frequencies for grouping and weighting | | --founderFreq: use founder frequencies for grouping and weighting |